#include <StrucMapping.hh>

Detailed Description

A class for mapping an arbitrary 'child' crystal structure as a deformation of a 'parent' crystal structure StrucMapper manages options for the mapping algorithm and mapping cost function It also caches some information about supercell lattices to improve speed of mapping multiple children crystals onto a single parent structure

Definition at line 404 of file StrucMapping.hh.

Public Types
enum	Options { none = 0 , strict = (1u << 0) , robust = (1u << 1) , sym_strain = (1u << 2) , sym_basis = (1u << 3) , soft_va_limit = (1u << 4) }

using	LatMapType = std::map< Index, std::vector< Lattice > >

Public Member Functions
	StrucMapper (StrucMapCalculatorInterface const &_calculator, double _lattice_weight=0.5, double _max_volume_change=0.5, int _options=0, double _cost_tol=TOL, double _min_va_frac=0., double _max_va_frac=1.)
	Construct and initialize a StrucMapper. More...

double	cost_tol () const
	Tolerance for determining if two mapping-cost values are identical. More...

double	xtal_tol () const
	Tolerance for initializing lattices. For now it is initialized to CASM::TOL. More...

double	lattice_weight () const

double	atomic_weight () const

void	set_lattice_weight (double _lw)

Index	lattice_transformation_range () const
	Max element considered for integer unimodular matrix transformations (which define orientation relationship of mapping) More...

void	set_lattice_transformation_range (Index _new_range)
	Max element considered for integer unimodular matrix transformations (which define orientation relationship of mapping) More...

void	set_symmetrize_lattice_cost (bool _sym_lat_cost)
	Flag that enables the calculation of a symmetrized lattice cost when performing the lattice maps. This cost only accounts for that part of the deformation gradient that breaks the symmetry of the parent crystal structure. More...

void	set_symmetrize_atomic_cost (bool _sym_atomic_cost, const SymOpVector &factor_group, const std::vector< Eigen::PermutationMatrix< Eigen::Dynamic, Eigen::Dynamic, Index >> &permutation_group)
	Flag that enables the calculation of a symmetrized atomic cost when performing the atomic maps. This cost only accounts for that part of the displacement field that breaks the symmetry of the parent crystal structure. More...

bool	symmetrize_lattice_cost () const

bool	symmetrize_atomic_cost () const

double	min_va_frac () const
	Returns the minimum fraction of sites allowed to be vacant in the mapping relation Vacancy fraction is used to constrain the mapping supercell search, but is only used when the supercell volume cannot is not uniquely determined by the number of each species in the child structure. More...

void	set_min_va_frac (double _min_va)
	Sets the minimum fraction of sites allowed to be vacant in the mapping relation Vacancy fraction is used to constrain the mapping supercell search, but is only used when the supercell volume cannot is not uniquely determined by the number of each species in the child structure. More...

double	max_va_frac () const
	Returns the maximum fraction of sites allowed to be vacant in the mapping relation Vacancy fraction is used to constrain the mapping supercell search, but is only used when the supercell volume cannot is not uniquely determined by the number of each species in the child structure. More...

void	set_max_va_frac (double _max_va)
	Sets the maximum fraction of sites allowed to be vacant in the mapping relation Vacancy fraction is used to constrain the mapping supercell search, but is only used when the supercell volume cannot is not uniquely determined by the number of each species in the child structure. More...

int	options () const
	returns bit flag of selected options for this StrucMapper More...

SimpleStructure const &	parent () const
	returns reference to parent structure More...

void	add_allowed_lattice (Lattice const &_lat)
	specify a superlattice of the parent to be searched during mapping More...

void	clear_allowed_lattices () const
	clear the list of allowed parent superlattices; all superlattices will be generated automatically, as needed (default) More...

bool	lattices_constrained () const
	returns true if the search of parent superlattices is constrained to a pre-specified list More...

void	set_filter (std::function< bool(Lattice const &, Lattice const &)> _filter_f)
	specify to use filtered lattices for mapping. The filter function is of the form bool filter(parent_lattice, proposed_lattice) where parent_lattice is the primitive lattice of the parent structure, and proposed_lattice is a proposed superlattice of the parent structure More...

void	unset_filter ()
	specify not to use filtered lattice for mapping More...

std::set< MappingNode >	map_ideal_struc (const SimpleStructure &child_struc, Index k=1, double max_cost=StrucMapping::big_inf(), double min_cost=-TOL, bool keep_invalid=false) const
	k-best mappings of ideal child structure onto parent structure Assumes that child_struc and parent_struc have lattices related by an integer transformation so that search over lattices can be replaced with simple matrix solution (faster than typical search) Atomic positions need not be ideal More...

std::set< MappingNode >	map_deformed_struc (const SimpleStructure &child_struc, Index k=1, double max_cost=StrucMapping::big_inf(), double min_cost=-TOL, bool keep_invalid=false, SymOpVector const &child_factor_group={SymOp::identity()}) const
	k-best mappings of arbitrary child structure onto parent structure, without simplifying assumptions If k and k+1, k+2, etc mappings have identical cost, k will be increased until k+n mapping has cost greater than mapping k More...

std::set< MappingNode >	map_deformed_struc_impose_lattice_vols (const SimpleStructure &child_struc, Index min_vol, Index max_vol, Index k=1, double max_cost=StrucMapping::big_inf(), double min_cost=-TOL, bool keep_invalid=false, SymOpVector const &child_factor_group={SymOp::identity()}) const
	k-best mappings of arbitrary child structure onto parent structure imposes simplifying assumption that solution is a superstructure of parent structure having integer volume on range [min_vol, max_vol] If k and k+1, k+2, etc mappings have identical cost, k will be increased until k+n mapping has cost greater than mapping k More...

std::set< MappingNode >	map_deformed_struc_impose_lattice (const SimpleStructure &child_struc, const Lattice &imposed_lat, Index k=1, double max_cost=StrucMapping::big_inf(), double min_cost=-TOL, bool keep_invalid=false, SymOpVector const &child_factor_group={SymOp::identity()}) const
	k-best mappings of arbitrary child structure onto parent structure imposes simplifying assumption that solution is THE superstructure of parent given by More...

std::set< MappingNode >	map_deformed_struc_impose_lattice_node (const SimpleStructure &child_struc, const LatticeNode &imposed_node, Index k=1, double max_cost=StrucMapping::big_inf(), double min_cost=-TOL, bool keep_invalid=false) const
	k-best mappings of arbitrary child structure onto parent structure imposes simplifying assumption that the lattice mapping is known and specified by More...

Index	k_best_maps_better_than (SimpleStructure const &child_struc, std::set< MappingNode > &queue, Index k=1, double max_cost=StrucMapping::big_inf(), double min_cost=-TOL, bool keep_invalid=false, bool keep_tail=false, bool no_partiton=false) const
	low-level function. Takes a queue of mappings and use it to seed a search for k-best total mappings. The seed mappings may be partial (having only LatticeNode specified, and not HungarianNode) or complete. The result is appended to More...

StrucMapCalculatorInterface const &	calculator () const

Private Member Functions
std::set< MappingNode >	_seed_k_best_from_super_lats (SimpleStructure const &child_struc, std::vector< Lattice > const &_parent_scels, std::vector< Lattice > const &_child_scels, Index k, double max_strain_cost, double min_strain_cost, SymOpVector const &child_factor_group={SymOp::identity()}) const
	generate list of partial mapping seeds (i.e., LatticeNode only) from a list of supercells of the parent structure and a list supercells of the child structure More...

std::set< MappingNode >	_seed_from_vol_range (SimpleStructure const &child_struc, Index k, Index min_vol, Index max_vol, double max_strain_cost, double min_strain_cost, SymOpVector const &child_factor_group={SymOp::identity()}) const
	construct partial mapping nodes (with uninitialized atomic_node) based on current settings considers supercells with integer volume between min_vol and max_vol More...

Index	_n_species (SimpleStructure const &sstruc) const
	returns number of species in a SimpleStructure given the current calculator settings. Use instead of sstruc.n_atom() for consistency More...

bool	_filter_lat (Lattice const &_parent_lat, Lattice const &_child_lat) const

std::pair< Index, Index >	_vol_range (const SimpleStructure &child_struc) const

std::vector< Lattice >	_lattices_of_vol (Index prim_vol) const

Private Attributes
notstd::cloneable_ptr< StrucMapCalculatorInterface >	m_calc_ptr

Eigen::MatrixXd	m_strain_gram_mat

double	m_lattice_weight

double	m_max_volume_change

int	m_options

double	m_cost_tol

double	m_xtal_tol

double	m_min_va_frac

double	m_max_va_frac

Index	m_lattice_transformation_range

bool	m_symmetrize_lattice_cost

bool	m_symmetrize_atomic_cost

bool	m_filtered

std::function< bool(Lattice const &, Lattice const &)>	m_filter_f

LatMapType	m_superlat_map
	Maps the supercell volume to a vector of Lattices with that volume. More...

LatMapType	m_allowed_superlat_map

Member Typedef Documentation

◆ LatMapType

using CASM::xtal::StrucMapper::LatMapType = std::map<Index, std::vector<Lattice> >

Definition at line 406 of file StrucMapping.hh.

Member Enumeration Documentation

◆ Options

enum CASM::xtal::StrucMapper::Options

Enumerator
none
strict
robust
sym_strain
sym_basis
soft_va_limit

Definition at line 408 of file StrucMapping.hh.

Constructor & Destructor Documentation

◆ StrucMapper()

CASM::xtal::StrucMapper::StrucMapper	(	StrucMapCalculatorInterface const &	_calculator,
		double	_lattice_weight = `0.5`,
		double	_max_volume_change = `0.5`,
		int	_options = `0`,
		double	_cost_tol = `TOL`,
		double	_min_va_frac = `0.`,
		double	_max_va_frac = `1.`
	)

Construct and initialize a StrucMapper.

Parameters

_calculator specialization of base class StrucMapCalculatorInterface, which controls the way that the cost_matrix and costs are calculated, determines validity of proposed mappings, and finalizes the representation of proposed mappings

Parameters

_lattice_weight free parameter 'w' in the cost function: total_cost = w*lattice_deformation+(1-w)*atomic_deformation can vary between 0 (completely basis-focused) and 1 (completely lattice-focused)

Parameters

_max_volume_change constrains the search space by assuming a limit on allowed volume change only taken into account when non-interstitial vacancies are allowed in parent structure

Parameters

_options

specify a combination of StrucMapper::Options using bitwise OR: Ex. _options=StrucMapper::robust|StrucMapper::strict Options are: 'robust': does not assume the imported structure might be ideal ('robust' is much slower for importing ideal structures, but if 'robust' is not set and a non-ideal structure is passed, this will be almost always be detected and robust methods will be used instead. Thus, 'robust' is slightly faster if imported Structures are not ideal)

'strict': prevents transformation into canonical form. Tries to preserve original orientation of imported structure if possible

Parameters

_cost_tol	tolerance for mapping comparisons
_min_va_frac	minimum fraction of vacant sites, below this fraction a mapping will not be considered
_max_va_frac	maximum fraction of vacant sites, above this fraction a mapping will not be considered

Definition at line 399 of file StrucMapping.cc.

Member Function Documentation

◆ _filter_lat()

bool CASM::xtal::StrucMapper::_filter_lat	(	Lattice const &	_parent_lat,
		Lattice const &	_child_lat
	)		const

inlineprivate

Definition at line 772 of file StrucMapping.hh.

◆ _lattices_of_vol()

std::vector< Lattice > CASM::xtal::StrucMapper::_lattices_of_vol ( Index prim_vol ) const

private

Definition at line 687 of file StrucMapping.cc.

◆ _n_species()

Index CASM::xtal::StrucMapper::_n_species ( SimpleStructure const & sstruc ) const

private

returns number of species in a SimpleStructure given the current calculator settings. Use instead of sstruc.n_atom() for consistency

Definition at line 427 of file StrucMapping.cc.

◆ _seed_from_vol_range()

std::set< MappingNode > CASM::xtal::StrucMapper::_seed_from_vol_range	(	SimpleStructure const &	child_struc,
		Index	k,
		Index	min_vol,
		Index	max_vol,
		double	max_strain_cost,
		double	min_strain_cost,
		SymOpVector const &	child_factor_group = `{SymOp::identity()}`
	)		const

private

construct partial mapping nodes (with uninitialized atomic_node) based on current settings considers supercells with integer volume between min_vol and max_vol

Definition at line 520 of file StrucMapping.cc.

◆ _seed_k_best_from_super_lats()

std::set< MappingNode > CASM::xtal::StrucMapper::_seed_k_best_from_super_lats	(	SimpleStructure const &	child_struc,
		std::vector< Lattice > const &	_parent_scels,
		std::vector< Lattice > const &	_child_scels,
		Index	k,
		double	max_strain_cost,
		double	min_strain_cost,
		SymOpVector const &	child_factor_group = `{SymOp::identity()}`
	)		const

private

generate list of partial mapping seeds (i.e., LatticeNode only) from a list of supercells of the parent structure and a list supercells of the child structure

Parameters

k	Number of k-best mapping relations to return
max_lattice_cost	Search will terminate once no lattice mappings better than max_lattice_cost are found
min_lattice_cost	All lattice mappings better than min_lattice_cost will be returned, without contributing to 'k'

Definition at line 852 of file StrucMapping.cc.

◆ _vol_range()

std::pair< Index, Index > CASM::xtal::StrucMapper::_vol_range ( const SimpleStructure & child_struc ) const

private

Definition at line 433 of file StrucMapping.cc.

◆ add_allowed_lattice()

void CASM::xtal::StrucMapper::add_allowed_lattice ( Lattice const & _lat )

inline

specify a superlattice of the parent to be searched during mapping

Definition at line 557 of file StrucMapping.hh.

◆ atomic_weight()

double CASM::xtal::StrucMapper::atomic_weight ( ) const

inline

Definition at line 484 of file StrucMapping.hh.

◆ calculator()

StrucMapCalculatorInterface const& CASM::xtal::StrucMapper::calculator ( ) const

inline

Definition at line 739 of file StrucMapping.hh.

◆ clear_allowed_lattices()

void CASM::xtal::StrucMapper::clear_allowed_lattices ( ) const

inline

clear the list of allowed parent superlattices; all superlattices will be generated automatically, as needed (default)

Definition at line 565 of file StrucMapping.hh.

◆ cost_tol()

double CASM::xtal::StrucMapper::cost_tol ( ) const

inline

Tolerance for determining if two mapping-cost values are identical.

Definition at line 476 of file StrucMapping.hh.

◆ k_best_maps_better_than()

Index CASM::xtal::StrucMapper::k_best_maps_better_than	(	SimpleStructure const &	child_struc,
		std::set< MappingNode > &	queue,
		Index	k = `1`,
		double	max_cost = `StrucMapping::big_inf()`,
		double	min_cost = `-TOL`,
		bool	keep_invalid = `false`,
		bool	keep_tail = `false`,
		bool	no_partiton = `false`
	)		const

low-level function. Takes a queue of mappings and use it to seed a search for k-best total mappings. The seed mappings may be partial (having only LatticeNode specified, and not HungarianNode) or complete. The result is appended to

Parameters

queue,and	partial and invalid mappings are removed from the queue. If k and k+1, k+2, etc mappings have identical cost, k will be increased until k+n mapping has cost greater than mapping k
child_struc	Input structure to be mapped onto parent structure
queue	list of partial mappings to seed search. Partial mappings are removed from list as they are searched finalized mappings are inserted into list as they are found.

Parameters

k	Number of k-best mapping relations to return
max_cost	Search will terminate once no mappings better than max_cost are found
min_cost	All mappings better than min_cost will be reported, without contributing to 'k'
keep_invalid	If true, invalid mappings are retained in output; otherwise they are discarded
keep_tail	If true, any partial or unresolved mappings at back of queue will be retained (they are deleted otherwise)
no_partition	If true, search over suboptimal basis permutations will be skipped (The optimal mapping will be found, but suboptimal mappings may be excluded in the k-best case. Degenerate permutations of atoms will not be identified.)

Returns: Index specifying the number of complete, valid mappings in the solution set

Definition at line 754 of file StrucMapping.cc.

◆ lattice_transformation_range()

Index CASM::xtal::StrucMapper::lattice_transformation_range ( ) const

inline

Max element considered for integer unimodular matrix transformations (which define orientation relationship of mapping)

Definition at line 492 of file StrucMapping.hh.

◆ lattice_weight()

double CASM::xtal::StrucMapper::lattice_weight ( ) const

inline

Definition at line 482 of file StrucMapping.hh.

◆ lattices_constrained()

bool CASM::xtal::StrucMapper::lattices_constrained ( ) const

inline

returns true if the search of parent superlattices is constrained to a pre-specified list

Definition at line 569 of file StrucMapping.hh.

◆ map_deformed_struc()

std::set< MappingNode > CASM::xtal::StrucMapper::map_deformed_struc	(	const SimpleStructure &	child_struc,
		Index	k = `1`,
		double	max_cost = `StrucMapping::big_inf()`,
		double	min_cost = `-TOL`,
		bool	keep_invalid = `false`,
		SymOpVector const &	child_factor_group = `{SymOp::identity()}`
	)		const

k-best mappings of arbitrary child structure onto parent structure, without simplifying assumptions If k and k+1, k+2, etc mappings have identical cost, k will be increased until k+n mapping has cost greater than mapping k

Parameters

child_struc	Input structure to be mapped onto parent structure
k	Number of k-best mapping relations to return
max_cost	Search will terminate once no mappings better than max_cost are found
min_cost	All mappings better than min_cost will be reported, without contributing to 'k'
keep_invalid	If true, invalid mappings are retained in output; otherwise they are discarded

Returns: std::set<MappingNode> a list of valid mappings, sorted first by cost, and then other attributes

Definition at line 622 of file StrucMapping.cc.

◆ map_deformed_struc_impose_lattice()

std::set< MappingNode > CASM::xtal::StrucMapper::map_deformed_struc_impose_lattice	(	const SimpleStructure &	child_struc,
		const Lattice &	imposed_lat,
		Index	k = `1`,
		double	max_cost = `StrucMapping::big_inf()`,
		double	min_cost = `-TOL`,
		bool	keep_invalid = `false`,
		SymOpVector const &	child_factor_group = `{SymOp::identity()}`
	)		const

k-best mappings of arbitrary child structure onto parent structure imposes simplifying assumption that solution is THE superstructure of parent given by

Parameters

imposed_lat.	Significantly faster than unconstrained search, but may miss best solution If k and k+1, k+2, etc mappings have identical cost, k will be increased until k+n mapping has cost greater than mapping k
child_struc	Input structure to be mapped onto parent structure
k	Number of k-best mapping relations to return
max_cost	Search will terminate once no mappings better than max_cost are found
min_cost	All mappings better than min_cost will be reported, without contributing to 'k'
keep_invalid	If true, invalid mappings are retained in output; otherwise they are discarded

Returns: std::set<MappingNode> a list of valid mappings, sorted first by cost, and then other attributes

Definition at line 654 of file StrucMapping.cc.

◆ map_deformed_struc_impose_lattice_node()

std::set< MappingNode > CASM::xtal::StrucMapper::map_deformed_struc_impose_lattice_node	(	const SimpleStructure &	child_struc,
		const LatticeNode &	imposed_node,
		Index	k = `1`,
		double	max_cost = `StrucMapping::big_inf()`,
		double	min_cost = `-TOL`,
		bool	keep_invalid = `false`
	)		const

k-best mappings of arbitrary child structure onto parent structure imposes simplifying assumption that the lattice mapping is known and specified by

Parameters

imposed_node.	This sets the lattice and setting that defines the mapping relation This assumption is much than unconstrained search, but may miss best solution If k and k+1, k+2, etc mappings have identical cost, k will be increased until k+n mapping has cost greater than mapping k
child_struc	Input structure to be mapped onto parent structure
k	Number of k-best mapping relations to return
max_cost	Search will terminate once no mappings better than max_cost are found
min_cost	All mappings better than min_cost will be reported, without contributing to 'k'
keep_invalid	If true, invalid mappings are retained in output; otherwise they are discarded

Returns: std::set<MappingNode> a list of valid mappings, sorted first by cost, and then other attributes

Definition at line 673 of file StrucMapping.cc.

◆ map_deformed_struc_impose_lattice_vols()

std::set< MappingNode > CASM::xtal::StrucMapper::map_deformed_struc_impose_lattice_vols	(	const SimpleStructure &	child_struc,
		Index	min_vol,
		Index	max_vol,
		Index	k = `1`,
		double	max_cost = `StrucMapping::big_inf()`,
		double	min_cost = `-TOL`,
		bool	keep_invalid = `false`,
		SymOpVector const &	child_factor_group = `{SymOp::identity()}`
	)		const

k-best mappings of arbitrary child structure onto parent structure imposes simplifying assumption that solution is a superstructure of parent structure having integer volume on range [min_vol, max_vol] If k and k+1, k+2, etc mappings have identical cost, k will be increased until k+n mapping has cost greater than mapping k

Parameters

child_struc	Input structure to be mapped onto parent structure
k	Number of k-best mapping relations to return
max_cost	Search will terminate once no mappings better than max_cost are found
min_cost	All mappings better than min_cost will be reported, without contributing to 'k'
keep_invalid	If true, invalid mappings are retained in output; otherwise they are discarded

Returns: std::set<MappingNode> a list of valid mappings, sorted first by cost, and then other attributes

Definition at line 634 of file StrucMapping.cc.

◆ map_ideal_struc()

std::set< MappingNode > CASM::xtal::StrucMapper::map_ideal_struc	(	const SimpleStructure &	child_struc,
		Index	k = `1`,
		double	max_cost = `StrucMapping::big_inf()`,
		double	min_cost = `-TOL`,
		bool	keep_invalid = `false`
	)		const

k-best mappings of ideal child structure onto parent structure Assumes that child_struc and parent_struc have lattices related by an integer transformation so that search over lattices can be replaced with simple matrix solution (faster than typical search) Atomic positions need not be ideal

Parameters

child_struc	Input structure to be mapped onto parent structure
k	Number of k-best mapping relations to return.
max_cost	Search will terminate once no mappings better than max_cost are found
min_cost	All mappings better than min_cost will be reported, without contributing to 'k'

Returns: std::set<MappingNode> a list of valid mappings, sorted first by cost, and then other attributes

Definition at line 573 of file StrucMapping.cc.

◆ max_va_frac()

double CASM::xtal::StrucMapper::max_va_frac ( ) const

inline

Returns the maximum fraction of sites allowed to be vacant in the mapping relation Vacancy fraction is used to constrain the mapping supercell search, but is only used when the supercell volume cannot is not uniquely determined by the number of each species in the child structure.

Definition at line 542 of file StrucMapping.hh.

◆ min_va_frac()

double CASM::xtal::StrucMapper::min_va_frac ( ) const

inline

Returns the minimum fraction of sites allowed to be vacant in the mapping relation Vacancy fraction is used to constrain the mapping supercell search, but is only used when the supercell volume cannot is not uniquely determined by the number of each species in the child structure.

Definition at line 530 of file StrucMapping.hh.

◆ options()

int CASM::xtal::StrucMapper::options ( ) const

inline

returns bit flag of selected options for this StrucMapper

Definition at line 551 of file StrucMapping.hh.

◆ parent()

SimpleStructure const & CASM::xtal::StrucMapper::parent ( ) const

returns reference to parent structure

Definition at line 514 of file StrucMapping.cc.

◆ set_filter()

void CASM::xtal::StrucMapper::set_filter ( std::function< bool(Lattice const &, Lattice const &)> _filter_f )

inline

specify to use filtered lattices for mapping. The filter function is of the form bool filter(parent_lattice, proposed_lattice) where parent_lattice is the primitive lattice of the parent structure, and proposed_lattice is a proposed superlattice of the parent structure

Definition at line 576 of file StrucMapping.hh.

◆ set_lattice_transformation_range()

void CASM::xtal::StrucMapper::set_lattice_transformation_range ( Index _new_range )

inline

Max element considered for integer unimodular matrix transformations (which define orientation relationship of mapping)

Definition at line 498 of file StrucMapping.hh.

◆ set_lattice_weight()

void CASM::xtal::StrucMapper::set_lattice_weight ( double _lw )

inline

Definition at line 486 of file StrucMapping.hh.

◆ set_max_va_frac()

void CASM::xtal::StrucMapper::set_max_va_frac ( double _max_va )

inline

Sets the maximum fraction of sites allowed to be vacant in the mapping relation Vacancy fraction is used to constrain the mapping supercell search, but is only used when the supercell volume cannot is not uniquely determined by the number of each species in the child structure.

Definition at line 548 of file StrucMapping.hh.

◆ set_min_va_frac()

void CASM::xtal::StrucMapper::set_min_va_frac ( double _min_va )

inline

Sets the minimum fraction of sites allowed to be vacant in the mapping relation Vacancy fraction is used to constrain the mapping supercell search, but is only used when the supercell volume cannot is not uniquely determined by the number of each species in the child structure.

Definition at line 536 of file StrucMapping.hh.

◆ set_symmetrize_atomic_cost()

void CASM::xtal::StrucMapper::set_symmetrize_atomic_cost	(	bool	_sym_atomic_cost,
		const SymOpVector &	factor_group,
		const std::vector< Eigen::PermutationMatrix< Eigen::Dynamic, Eigen::Dynamic, Index >> &	permutation_group
	)

inline

Flag that enables the calculation of a symmetrized atomic cost when performing the atomic maps. This cost only accounts for that part of the displacement field that breaks the symmetry of the parent crystal structure.

Definition at line 514 of file StrucMapping.hh.

◆ set_symmetrize_lattice_cost()

void CASM::xtal::StrucMapper::set_symmetrize_lattice_cost ( bool _sym_lat_cost )

inline

Flag that enables the calculation of a symmetrized lattice cost when performing the lattice maps. This cost only accounts for that part of the deformation gradient that breaks the symmetry of the parent crystal structure.

Definition at line 506 of file StrucMapping.hh.

◆ symmetrize_atomic_cost()

bool CASM::xtal::StrucMapper::symmetrize_atomic_cost ( ) const

inline

Definition at line 524 of file StrucMapping.hh.

◆ symmetrize_lattice_cost()

bool CASM::xtal::StrucMapper::symmetrize_lattice_cost ( ) const

inline

Definition at line 523 of file StrucMapping.hh.

◆ unset_filter()

void CASM::xtal::StrucMapper::unset_filter ( )

inline

specify not to use filtered lattice for mapping

Definition at line 584 of file StrucMapping.hh.

◆ xtal_tol()

double CASM::xtal::StrucMapper::xtal_tol ( ) const

inline

Tolerance for initializing lattices. For now it is initialized to CASM::TOL.

Definition at line 480 of file StrucMapping.hh.

Member Data Documentation

◆ m_allowed_superlat_map

LatMapType CASM::xtal::StrucMapper::m_allowed_superlat_map

mutableprivate

Definition at line 801 of file StrucMapping.hh.

◆ m_calc_ptr

notstd::cloneable_ptr<StrucMapCalculatorInterface> CASM::xtal::StrucMapper::m_calc_ptr

private

Definition at line 779 of file StrucMapping.hh.

◆ m_cost_tol

double CASM::xtal::StrucMapper::m_cost_tol

private

Definition at line 786 of file StrucMapping.hh.

◆ m_filter_f

std::function<bool(Lattice const &, Lattice const &)> CASM::xtal::StrucMapper::m_filter_f

private

Definition at line 797 of file StrucMapping.hh.

◆ m_filtered

bool CASM::xtal::StrucMapper::m_filtered

private

Definition at line 796 of file StrucMapping.hh.

◆ m_lattice_transformation_range

Index CASM::xtal::StrucMapper::m_lattice_transformation_range

private

Definition at line 791 of file StrucMapping.hh.

◆ m_lattice_weight

double CASM::xtal::StrucMapper::m_lattice_weight

private

Definition at line 783 of file StrucMapping.hh.

◆ m_max_va_frac

double CASM::xtal::StrucMapper::m_max_va_frac

private

Definition at line 789 of file StrucMapping.hh.

◆ m_max_volume_change

double CASM::xtal::StrucMapper::m_max_volume_change

private

Definition at line 784 of file StrucMapping.hh.

◆ m_min_va_frac

double CASM::xtal::StrucMapper::m_min_va_frac

private

Definition at line 788 of file StrucMapping.hh.

◆ m_options

int CASM::xtal::StrucMapper::m_options

private

Definition at line 785 of file StrucMapping.hh.

◆ m_strain_gram_mat

Eigen::MatrixXd CASM::xtal::StrucMapper::m_strain_gram_mat

private

Definition at line 781 of file StrucMapping.hh.

◆ m_superlat_map

LatMapType CASM::xtal::StrucMapper::m_superlat_map

mutableprivate

Maps the supercell volume to a vector of Lattices with that volume.

Definition at line 800 of file StrucMapping.hh.

◆ m_symmetrize_atomic_cost

bool CASM::xtal::StrucMapper::m_symmetrize_atomic_cost

private

Definition at line 794 of file StrucMapping.hh.

◆ m_symmetrize_lattice_cost

bool CASM::xtal::StrucMapper::m_symmetrize_lattice_cost

private

Definition at line 793 of file StrucMapping.hh.

◆ m_xtal_tol

double CASM::xtal::StrucMapper::m_xtal_tol

private

Definition at line 787 of file StrucMapping.hh.

The documentation for this class was generated from the following files:

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/crystallography/StrucMapping.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/crystallography/StrucMapping.cc

Detailed Description

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ LatMapType

Member Enumeration Documentation

◆ Options

Constructor & Destructor Documentation

◆ StrucMapper()

Member Function Documentation

◆ _filter_lat()

◆ _lattices_of_vol()

◆ _n_species()

◆ _seed_from_vol_range()

◆ _seed_k_best_from_super_lats()

◆ _vol_range()

◆ add_allowed_lattice()

◆ atomic_weight()

◆ calculator()

◆ clear_allowed_lattices()

◆ cost_tol()

◆ k_best_maps_better_than()

◆ lattice_transformation_range()

◆ lattice_weight()

◆ lattices_constrained()

◆ map_deformed_struc()

◆ map_deformed_struc_impose_lattice()

◆ map_deformed_struc_impose_lattice_node()

◆ map_deformed_struc_impose_lattice_vols()

◆ map_ideal_struc()

◆ max_va_frac()

◆ min_va_frac()

◆ options()

◆ parent()

◆ set_filter()

◆ set_lattice_transformation_range()

◆ set_lattice_weight()

◆ set_max_va_frac()

◆ set_min_va_frac()

◆ set_symmetrize_atomic_cost()

◆ set_symmetrize_lattice_cost()

◆ symmetrize_atomic_cost()

◆ symmetrize_lattice_cost()

◆ unset_filter()

◆ xtal_tol()

Member Data Documentation

◆ m_allowed_superlat_map

◆ m_calc_ptr

◆ m_cost_tol

◆ m_filter_f

◆ m_filtered

◆ m_lattice_transformation_range

◆ m_lattice_weight

◆ m_max_va_frac

◆ m_max_volume_change

◆ m_min_va_frac

◆ m_options

◆ m_strain_gram_mat

◆ m_superlat_map

◆ m_symmetrize_atomic_cost

◆ m_symmetrize_lattice_cost

◆ m_xtal_tol